rs3025316

Variant names:

• chr9-133594421-T-C
• rs3025316
• NM_001080515.3:c.-23-14175A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080515.3(FAM163B):​c.-23-14175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,236 control chromosomes in the GnomAD database, including 493 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.068 (493 hom., cov: 32)
• Consequence: FAM163B NM_001080515.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 7 publications found

Genes affected

FAM163B (HGNC:33277): (family with sequence similarity 163 member B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM163B	NM_001080515.3	c.-23-14175A>G		intron_variant	Intron 1 of 2	ENST00000673969.1	NP_001073984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM163B	ENST00000673969.1	c.-23-14175A>G		intron_variant	Intron 1 of 2		NM_001080515.3	ENSP00000501259.1

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10308 AN: 152120 Hom.: 493 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0709

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0677 AC: 10307 AN: 152236 Hom.: 493 Cov.: 32 AF XY: 0.0628 AC XY: 4674 AN XY: 74440

African (AFR) AF: 0.0206 AC: 854 AN: 41540

American (AMR) AF: 0.0699 AC: 1069 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5172

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4820

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10622

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7641 AN: 68008

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0969 Hom.: 1587

Bravo AF: 0.0672

Asia WGS AF: 0.0120 AC: 41 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3025316; hg19: chr9-136459543;